Seroatlas · Human Serome Atlas

SCLT1

Sodium channel and clathrin linker 1

Also known as: FLJ30655, hCAP-1A, SCLT1_HUMAN

Cross-references: UniProt · Ensembl · Human Protein Atlas · GeneCards · NCBI Gene

Protein identityUniProt · HPA

UniProt accession: Q96NL6
Gene: SCLT1
Ensembl: ENSG00000151466
Chromosome: 4
Canonical length: 688 aa
Protein class: Predicted intracellular proteins
Subcellular location: Microtubules,Basal body,Cytosol

OverviewNCBI Gene

This gene encodes an adaptor protein. Studies of a related gene in rat suggest that the encoded protein functions to link clathrin to the sodium channel protein type 10 subunit alpha protein. The encoded protein has also been identified as a component of distal appendages of centrioles that is necessary for ciliogenesis. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Jul 2014]

Canonical amino-acid sequenceUniProt

688 residues, UniProt reviewed canonical sequence.

>Q96NL6|SCLT1
     1  MAAEIDFLRE QNRRLNEDFR RYQMESFSKY SSVQKAVCQG EGDDTFENLV FDQSFLAPLV
    61  TEYDKHLGEL NGQLKYYQKQ VGEMKLQLEN VIKENERLHS ELKDAVEKKL EAFPLGTEVG
   121  TDIYADDETV RNLQEQLQLA NQEKTQAVEL WQTVSQELDR LHKLYQEHMT EAQIHVFESQ
   181  KQKDQLFDFQ QLTKQLHVTN ENMEVTNQQF LKTVTEQSVI IEQLRKKLRQ AKLELRVAVA
   241  KVEELTNVTE DLQGQMKKKE KDVVSAHGRE EASDRRLQQL QSSIKQLEIR LCVTIQEANQ
   301  LRTENTHLEK QTRELQAKCN ELENERYEAI VRARNSMQLL EEANLQKSQA LLEEKQKEED
   361  IEKMKETVSR FVQDATIRTK KEVANTKKQC NIQISRLTEE LSALQMECAE KQGQIERVIK
   421  EKKAVEEELE KIYREGRGNE SDYRKLEEMH QRFLVSERSK DDLQLRLTRA ENRIKQLETD
   481  SSEEISRYQE MIQKLQNVLE SERENCGLVS EQRLKLQQEN KQLRKETESL RKIALEAQKK
   541  AKVKISTMEH EFSIKERGFE VQLREMEDSN RNSIVELRHL LATQQKAANR WKEETKKLTE
   601  SAEIRINNLK SELSRQKLHT QELLSQLEMA NEKVAENEKL ILEHQEKANR LQRRLSQAEE
   661  RAASASQQLS VITVQRRKAA SLMNLENI

LocalizationUniProt · AlphaFold · HPA

Whether an antibody against SCLT1 can act on the native protein depends on physical access: surface and secreted proteins are reachable by circulating antibodies, intracellular proteins usually are not.

Antibody reachability: Cell surface
Secreted: No
Transmembrane segments: 0
Mean surface accessibility (rSASA): 0.5
Highest tissue expression: 14 nTPM

Expression across tissuesHPA

Tissue

bone marrow: 14 nTPM
thymus: 8.2 nTPM
spleen: 7.1 nTPM
lymph node: 6.9 nTPM
tonsil: 6.3 nTPM
appendix: 6.1 nTPM

Single-cell type

neutrophils: 1,017 nCPM
neutrophil progenitors: 416 nCPM
megakaryocyte progenitors: 367 nCPM
mast cells: 342 nCPM
innate lymphoid cells: 333 nCPM
monocytes: 324 nCPM

Immune cell

neutrophil: 66 nTPM
eosinophil: 37 nTPM
non-classical monocyte: 31 nTPM
intermediate monocyte: 25 nTPM
basophil: 18 nTPM
classical monocyte: 17 nTPM

Brain region

cerebellum: 26 nTPM
thalamus: 22 nTPM
cerebral cortex: 21 nTPM
medulla oblongata: 21 nTPM
spinal cord: 20 nTPM
midbrain: 20 nTPM

DiseaseUniProt · ClinVar · IEDB · PubMed

Four sources answering four different questions about SCLT1.

Disease | GeneticClinVar

52 pathogenic / likely-pathogenic of 577 ClinVar records.

Conditions with pathogenic or likely-pathogenic variants.

Genetic constraint and essentialitygnomAD · DepMap

Does the body need this protein intact? Low LOEUF or a strong DepMap dependency means loss or blockade of the protein is likely to be felt.

gnomAD LOEUF (loss-of-function intolerance): 0.89
gnomAD pLI: 0
gnomAD missense Z: -0.27
DepMap mean gene effect: 0.06
DepMap dependency class: none

Cancer expressionTCGA

Across TCGA tumor cohorts, this protein is over-expressed in roughly 4% of surveyed tumor types (aggregate summary; per-cohort expression, alteration, and survival load in the interactive view).

OntologyGO

Biological processes

Molecular functions

Cellular components

Protein domainsUniProt · Pfam · InterPro

Sodium channel and clathrin linker 1

KeywordsUniProt

InteractionsUniProt · HPA

Protein binding partners of SCLT1 in the human serome: UniProt-annotated complex subunits plus reported interactors. Each links to its own Seroatlas record.

SCN10A

Antibody and autoantibody relevanceSeroatlas analysis

Seroatlas reads SCLT1 as an antibody target. Whether an autoantibody or antibody against SCLT1 could matter depends on whether native SCLT1 is physically reachable, whether the body needs it intact, and whether it acts in a disease-relevant tissue.

SCLT1 is annotated at the cell surface, where native SCLT1 is exposed to circulating antibodies and is a prime autoantibody target that could block, deplete, or overstimulate it.

Annotation status

The present source text does not explicitly label SCLT1 as an autoantigen. Seroatlas presents hypothesis context only and does not manufacture a known-serology claim.

Loading the interactive Seroatlas protein explorer...